9-131072668-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_006059.4(LAMC3):c.3250G>C(p.Glu1084Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00508 in 1,611,370 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006059.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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LAMC3 | NM_006059.4 | c.3250G>C | p.Glu1084Gln | missense_variant | Exon 19 of 28 | ENST00000361069.9 | NP_006050.3 | |
LAMC3 | XM_011518121.2 | c.3250G>C | p.Glu1084Gln | missense_variant | Exon 19 of 28 | XP_011516423.1 | ||
LAMC3 | XM_006716921.3 | c.3250G>C | p.Glu1084Gln | missense_variant | Exon 19 of 23 | XP_006716984.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00348 AC: 529AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00341 AC: 843AN: 247176Hom.: 1 AF XY: 0.00364 AC XY: 488AN XY: 133964
GnomAD4 exome AF: 0.00525 AC: 7663AN: 1459132Hom.: 35 Cov.: 36 AF XY: 0.00537 AC XY: 3896AN XY: 725758
GnomAD4 genome AF: 0.00347 AC: 529AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.00341 AC XY: 254AN XY: 74446
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:6
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LAMC3: BP4, BS2 -
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not specified Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Occipital pachygyria and polymicrogyria Benign:1
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LAMC3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at